An assessment of compositional methods for the analysis of DNA methylation-based deconvolution estimates.

DNA methylation (DNAm)-based deconvolution estimates contain relative data, forming a composition, that standard methods (testing directly on cell proportions) are ill-suited to handle. In this study we examined the performance of an alternative method, analysis of compositions of microbiomes (ANCOM), for the analysis of DNAm-based deconvolution estimates. We performed two different simulation studies comparing ANCOM to a standard approach (two sample -test performed directly on cell proportions) and analyzed a real-world data from the Women's Health Initiative to evaluate the applicability of ANCOM to DNAm-based deconvolution estimates.

Interventions for insomnia in cancer patients and survivors-a comprehensive systematic review and meta-analysis.

Background: Considering the persistent nature and higher prevalence of insomnia in cancer patients and survivors compared with the general population, there is a need for effective management strategies. This systematic review and meta-analysis aimed to comprehensively evaluate the available evidence for the efficacy of pharmacological and nonpharmacological interventions for insomnia in adult cancer patients and survivors.

Methods: Following the PRISMA guidelines, we analyzed data from 61 randomized controlled trials involving 6528 participants.

Summer Cancer Research Experience for High School Students from Historically Marginalized Populations in Kansas City.

The Accelerate Cancer Education (ACE) summer research program at The University of Kansas Cancer Center (KUCC) is a six-week, cancer-focused, summer research experience for high school students from historically marginalized populations in the Kansas City metropolitan area. Cancer affects all populations and continues to be the second leading cause of death in the United States, and a large number of disparities impact racial and ethnic minorities, including increased cancer incidence and mortality. Critically, strategies to bolster diversity, equity, inclusion, and accessibility are needed to address persistent cancer disparities.

Neutrophil extracellular traps linked to idiopathic pulmonary fibrosis severity and survival.

Background: Idiopathic pulmonary fibrosis (IPF) leads to progressive loss of lung function and mortality. Understanding mechanisms and markers of lung injury in IPF is paramount to improving outcomes for these patients. Despite the lack of systemic involvement in IPF, many analyses focus on identifying prognostic markers.

Enrichment of a neutrophil-like monocyte transcriptional state in glioblastoma myeloid suppressor cells.

Glioblastomas (GBM) are lethal central nervous system cancers associated with tumor and systemic immunosuppression. Heterogeneous monocyte myeloid-derived suppressor cells (M-MDSC) are implicated in the altered immune response in GBM, but M-MDSC ontogeny and definitive phenotypic markers are unknown. Using single-cell transcriptomics, we revealed heterogeneity in blood M-MDSC from GBM subjects and an enrichment in a transcriptional state reminiscent of neutrophil-like monocytes (NeuMo), a newly described pathway of monopoiesis in mice.

Comprehensive exploration of JQ1 and GSK2801 targets in breast cancer using network pharmacology and molecular modeling approaches.

JQ1 and GSK2801 are bromo domain inhibitors (BDI) known to exhibit enhanced anti-cancer activity when combined with other agents. However, the underlying molecular mechanisms behind such enhanced activity remain unclear. We used network-pharmacology approaches to understand the shared molecular mechanisms behind the enhanced activity of JQ1 and GSK2801 when used together to treat breast cancer (BC).

optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis.

Summary: The Tapestri platform offers DNA and protein analysis at the single-cell level. Integrating both types of data is beneficial for studying multiple cell populations in heterogeneous microenvironments, such as tumor tissues. Here, we present optima, an R package for the processing and analysis of data generated from the Tapestri platform.

Assessment of immune cell profiles among post-menopausal women in the Women's Health Initiative using DNA methylation-based methods.

Background: Over the past decade, DNA methylation (DNAm)-based deconvolution methods that leverage cell-specific DNAm markers of immune cell types have been developed to provide accurate estimates of the proportions of leukocytes in peripheral blood. Immune cell phenotyping using DNAm markers, termed immunomethylomics or methylation cytometry, offers a solution for determining the body's immune cell landscape that does not require fresh blood and is scalable to large sample sizes. Despite significant advances in DNAm-based deconvolution, references at the population level are needed for clinical and research interpretation of these additional immune layers.

Assessing Breast Cancer Molecular Subtypes Using Extracellular Vesicles' mRNA.

Extracellular vesicles (EVs) carry RNA cargo that is believed to be associated with the cell-of-origin and thus have the potential to serve as a minimally invasive liquid biopsy marker for supplying molecular information to guide treatment decisions (i.e., precision medicine).

Autonomic function and inflammation in pregnant women participating in a randomized controlled study of Mindfulness Based Childbirth and Parenting.

Background: Pregnancy and childbirth are significant events in many women's lives, and the prevalence of depressive symptoms increases during this vulnerable period. Apart from well documented cognitive, affective, and somatic symptoms, stress and depression are associated with physiological changes, such as reduced heart-rate variability (HRV) and activation of the inflammatory response system. Mindfulness Based Interventions may potentially have an effect on both HRV, inflammatory biomarkers, and self-assessed mental health.

Comparing the efficacy of mindfulness-based therapy and cognitive-behavioral therapy for depression in head-to-head randomized controlled trials: A systematic review and meta-analysis of equivalence.

Background: While Cognitive Behavioral Therapy (CBT) is recommended as first-line treatment for depression, a significant minority do not show an adequate treatment response. Despite evidence for the efficacy of Mindfulness-Based Therapies (MBT) both in treating current depression and preventing relapse, it remains unknown whether MBT and CBT are equivalent in the treatment of current depression.

Methods: Five databases were searched for randomized controlled trials (RCTs) directly comparing MBT with CBT and including depression as primary or secondary outcome.

Comparative study of two re-embedding methods on the ultrastructure of corneal tissue.

Purpose: To expand the routine of pathological diagnostics of surgical keratoplasty specimens via transmission electron microscopy. The target was to identify the best re-embedding method for optimal structural preservation of formalin fixed paraffin embedded (FFPE) corneal tissue re-embedded into resin for ultrastructural analysis.

Basic Procedures: Bovine FFPE corneal tissue was re-embedded into resin with either a rapid osmium-free four-hour-method or a four-day-routine-method known from nephropathology, compared with primary resin embedded bovine corneal tissue.

DNA methylation as a pharmacodynamic marker of glucocorticoid response and glioma survival.

Assessing individual responses to glucocorticoid drug therapies that compromise immune status and affect survival outcomes in neuro-oncology is a great challenge. Here we introduce a blood-based neutrophil dexamethasone methylation index (NDMI) that provides a measure of the epigenetic response of subjects to dexamethasone. This marker outperforms conventional approaches based on leukocyte composition as a marker of glucocorticoid response.

Clinicopathological Correlation of Microbial Keratitis and Ahead: Is There a Corneal Sepsis?

Microbial, infectious keratitis is a relevant indication for penetrating keratoplasty. The requirement for transplantation results in histopathological examination of the entire thickness of the cornea. Although the clinical diagnosis is not always possible to confirm, pathology can support diagnostic evidence of clinical presentation and pathogenesis.

The 2019-2020 Khalili (Iran) Earthquake Sequence-Anthropogenic Seismicity in the Zagros Simply Folded Belt?

We investigate the origin of a long-lived earthquake cluster in the Fars arc of the Zagros Simply Folded Belt that is colocated with the major Shanul natural gas field. The cluster emerged in January 2019 and initially comprised small events of ∼ 3-4. It culminated on 9 June 2020 with a pair of 5.

Mediators of acceptance and mindfulness-based therapies for anxiety and depression: A systematic review and meta-analysis.

Acceptance and mindfulness-based therapies have shown efficacy in the treatment of anxiety and depression. Arguably, acceptance and mindfulness-based therapies target core processes in anxiety and depression by increasing mindful attention, decentering, and acceptance. The present study identified randomized controlled trials of acceptance and mindfulness-based therapies for anxiety and depression.

A core of differentially methylated CpG loci in gMDSCs isolated from neonatal and adult sources.

Background: Myeloid-derived suppressor cells (MDSCs), which include monocytic (mMDSCs) and granulocytic (gMDSCs) cells, are an immunosuppressive, heterogeneous population of cells upregulated in cancer and other pathologic conditions, in addition to normal conditions of stress. The origin of MDSCs is debated, and the regulatory pattern responsible for gMDSC differentiation remains unknown. Since DNA methylation (DNAm) contributes to lineage differentiation, we have investigated whether it contributes to the acquisition of the gMDSC phenotype.

Low variability in the underlying cellular landscape adversely affects the performance of interaction-based approaches for conducting cell-specific analyses of DNA methylation in bulk samples.

Statistical methods that allow for cell type specific DNA methylation (DNAm) analyses based on bulk-tissue methylation data have great potential to improve our understanding of human disease and have created unprecedented opportunities for new insights using the wealth of publicly available bulk-tissue methylation data. These methodologies involve incorporating interaction terms formed between the phenotypes/exposures of interest and proportions of the cell types underlying the bulk-tissue sample used for DNAm profiling. Despite growing interest in such "interaction-based" methods, there has been no comprehensive assessment how variability in the cellular landscape across study samples affects their performance.

Ethylenediamine Catalyzes Nitromethane Shock-to-Detonation in Two Distinct Ways.

Adding amines to liquid nitromethane (NM) is known to lower the threshold for the shock-to-detonation transition because amines catalyze proton transfer reactions that are the initial steps in the energy release process. We studied NM with 1 wt % ethylenediamine (NM/EDA) with 4 ns input shocks using time and space resolved diagnostics: photon Doppler velocimetry (PDV), optical pyrometry, and nanosecond video imaging. The 4 ns shocks are fast enough to time-resolve the reaction kinetics and the shock-to-detonation transition.

Epidural Analgesia or Oxytocin, but Not Oxytocin Alone, Administered During Birth Disturbs Infant Pre-feeding and Sucking Behaviors and Maternal Oxytocin Levels in Connection With a Breastfeed Two Days Later.

This work aimed to study consequences of medical interventions in connection with birth on infant pre-feeding and feeding behaviors and on maternal oxytocin levels in connection with a breastfeed 2 days later. Mothers and their full-term newborns ( = 41) were videotaped during a breastfeed 2 days after birth. Duration and quality of rooting [Infant Breastfeeding Assessment Tool (IBFAT)] were assessed.

Internet-delivered Mindfulness-Based Cognitive Therapy for anxiety and depression in cancer survivors: Predictors of treatment response.

Background: The present study investigates possible predictors of treatment response in an Internet-delivered Mindfulness-Based Cognitive Therapy (iMBCT) intervention with therapist support. This iMBCT program, a fully online delivered intervention with asynchronous therapist support, has previously been shown to be efficacious in reducing symptoms of anxiety and depression in women treated for breast cancer and men treated for prostate cancer.

Methods: Eighty-two breast- and prostate cancer survivors experiencing psychological distress received 8 weeks of therapist-guided iMBCT.

Short-term psychodynamic infant-parent interventions at Child health centers: Outcomes on parental depression and infant social-emotional functioning.

Randomized controlled trials (RCTs) demonstrate efficacy of parent-infant psychotherapy, but its applicability and effectiveness in public health care are less known. The method followed is Naturalistic study evaluating Short-term Psychodynamic Infant-Parent Interventions at Child Health Centers (SPIPIC) in Stockholm, Sweden. One hundred distressed mothers with infants were recruited by supervised nurses.

Evolutionary Analysis of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reveals Genomic Divergence with Implications for Universal Vaccine Efficacy.

Coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is one of the pressing contemporary public health challenges. Investigations into the genomic structure of SARS-CoV-2 may inform ongoing vaccine development efforts and/or provide insights into vaccine efficacy to fight against COVID-19. Evolutionary analysis of 540 genomes spanning 20 different countries/territories was conducted and revealed an increase in the genomic divergence across successive generations.

Ewing sarcoma family of tumors-derived small extracellular vesicle proteomics identify potential clinical biomarkers.

Purpose: Ewing Sarcoma Family of Tumors (ESFT), the second most common pediatric osseous malignancy, are characterized by the pathognomonic chromosomal translocation. Outside of tumor biopsy, no clinically relevant ESFT biomarkers exist. Additionally, tumor burden assessment at diagnosis, monitoring of disease responsiveness to therapy, and detection of disease recurrence are limited to radiographic imaging.

The nine stages of skin-to-skin: practical guidelines and insights from four countries.

Incorporating systematic evidence with clinical expertise is a key element in the quest to improve quality of care and patient outcomes. The evidence supporting skin-to-skin contact in the first hour after birth is robust and includes significantly improved outcomes for both mother and infant. This paper compares available iterative data about newborn behaviour in the first hour after birth to further describe the observable behaviour pattern and to provide clinical insight for further research.